Array assays between surface bound binding agents or probes and target molecules in solution may be used to detect the presence of particular biopolymers. The surface-bound probes may be oligonucleotides, peptides, polypeptides, proteins, antibodies or other molecules capable of binding with target molecules in solution. Such binding interactions are the basis for many of the methods and devices used in a variety of different fields, e.g., genomics (in sequencing by hybridization, SNP detection, differential gene expression analysis, identification of novel genes, gene mapping, finger printing, etc.) and proteomics.
One typical array assay method involves biopolymeric probes immobilized in an array on a substrate such as a glass substrate or the like to provide an array assembly. A solution containing or suspected of containing analytes that bind with the attached probes is placed in contact with the one or more arrays of the array assembly. In many instances, a second substrate is positioned thereon, with a separator or the like therebetween, to form a sealed assay area around the one or more arrays of the assay assembly. This structure is oftentimes placed in a suitable environment to maintain proper array assay conditions, e.g., an incubator or the like, for the array assay protocol.
Usually, the targets in the solution, if present, bind to the complementary probes on the substrate to form a binding complex. The pattern of binding by target molecules to biopolymer probe features or spots on the substrate produces a pattern on the surface of the substrate and provides desired information about the sample. In most instances, the target molecules are labeled with a detectable tag such as a fluorescent tag, chemiluminescent tag or radioactive tag. The resultant binding interaction or complexes of binding pairs are then detected and read or interrogated, for example by optical means, although other methods may also be used. For example, laser light may be used to excite fluorescent tags, generating a signal only in those spots on the biochip that have a target molecule and thus a fluorescent tag bound to a probe molecule. This pattern may then be digitally scanned for computer analysis.
In certain instances, unwanted gaseous bubbles may be inadvertently formed or introduced into the area about the one or more arrays. These bubbles may deleteriously interfere with the performance of the assay, especially if a small fluid gap is maintained between the array assembly and the second substrate positioned in opposition thereto. For example, such bubbles may interfere with the binding of a target to its binding pair member probe.
These bubbles may be formed or introduced into the array assay area by any of a number of different mechanisms. For example, a fluidic sample (i.e., a fluid that includes or is suspected of including one or more targets) may be introduced to an array by manual injection (e.g., with a pipette, syringe or the like) or by automated injection. Bubbles may be the result of trapped air in the area assay chamber after sample introduction to that area. These bubbles may be trapped by the geometry of the array assay chamber or, in the case of gas permeable gasket structures that form an array assay chamber, within the assay chamber (i.e., a gasket seal). Bubbles may form from the introduction method such as in a pipette tip, sample introduction line, and the like. Unwanted bubbles may also form when the temperature of a dissolved gas-saturated fluidic sample is elevated to a higher temperature and/or when the fluidic sample is exposed to a lower pressure during the performance of an array assay. Bubbles may also be formed by rectified diffusion when mixing of the fluidic sample, if employed, produces a cyclic pressure variation.
Prior attempts have been employed to eliminate or minimize bubbles from an array assay fluid include degassing the fluid prior to introduction to an array (see for example U.S. patent application Ser. No. 20010041357A1). However, this approach does not provide a complete solution. For example, employing such a technique requires the fluid to go through a separate degassing process before introduction to the array. This separate degassing process may not remove all the dissolved gas and/or the fluid may absorb gas between the time it is degassed and the time it is introduced to an array and an array assay is performed. That is, bubbles may be formed after introduction of the fluid to the array, e.g., during the performance of the array assay, which bubbles would not be addressed using a pre-sample introduction degassing method. Another previously attempted method uses a porous hydrophobic membrane as a vent for degassing (see for example international publication WO2002097398A2). However, this method is not effective for small fluid gap (less than about 200 micrometers) chambers or channels. Bubbles, introduced or formed in the chamber are often not mobile even with mixing when stuck in a narrow gap, which mobility is necessary for the effective use of such vent degassing methods.
Thus, there continues to be an interest in the development of new devices and methods for performing array-based assays. Of particular interest would be the development of devices and methods that effectively remove dissolved gas and/or bubbles from a fluid for use in an array assay, for example during the performance of the array assay. Device and methods that are easy to implement for use in an array assay protocol, do not add significant cost to array based assays, and which may be employed in a variety of different array assays would be particularly advantageous.